Measurement precision and uncertainty estimation are important factors for all residual stress measurement techniques. The values of these quantities can help to determine whether a particular measurement technique would be viable option. This paper determines the precision of hole-drilling residual stress measurement using repeatability studies and develops an updated uncertainty estimator. Two repeatability studies were performed on test specimens extracted from aluminum and titanium shot peened plates. Each repeatability study included 12 hole-drilling measurements performed using a bespoke automated milling machine. Repeatability standard deviations were determined for each population. The repeatability studies were replicated using a commercially available manual hole-drilling milling machine. An updated uncertainty estimator was developed and was assessed using an acceptance criterion. The acceptance criterion compared an expected percentage of points (68%) to the fraction of points in the stress versus depth profile where the measured stresses ± its total uncertainty contained the mean stress of the repeatability studies. Both repeatability studies showed larger repeatability standard deviations at the surface that decay quickly (over about 0.3 mm). The repeatability standard deviation was significantly smaller in the aluminum plate (max ≈ 15 MPa, RMS ≈ 6.4 MPa) than in the titanium plate (max ≈ 60 MPa, RMS ≈ 21.0 MPa). The repeatability standard deviations were significantly larger when using the manual milling machine in the aluminum plate (RMS ≈ 21.7 MPa), and for the titanium plate (RMS ≈ 18.9 MPa). The single measurement uncertainty estimate met a defined acceptance criterion based on the confidence interval of the uncertainty estimate.